Statistical Methods for Detecting Deletions Using SNP Genotypes in Case-Control Studies

• Activity Number: 486
• Type: Contributed
• Date/Time: Thursday, August 7, 2008 : 8:30 AM to 10:20 AM
• Sponsor: Biometrics Section
• Author(s): Chih-Chieh Wu*+ and Sanjay Shete and Bo Peng and Jianzhong Ma and Christopher I. Amos
• Companies: The University of Texas M.D. Anderson Cancer Center and The University of Texas M.D. Anderson Cancer Center and The University of Texas M.D. Anderson Cancer Center and The University of Texas M.D. Anderson Cancer Center and The University of Texas M.D. Anderson Cancer Center
• Keywords: genetic ; case-control studies ; deletion ; genotype

Abstract

Recent studies show that genomic deletions can play an important and crucial role in genetic basis of complex traits. Existing methods for identifying genomic deletions from genetic markers are generally based on the observation of Mendelian transmission failure in parents-child trios, Hardy-Weinberg disequilibrium, and null genotypes. We propose statistical methods that use SNP genotype data to detect genomic deletions and to assess the association with the disease of interest. One approach assesses the excess of homozygosity of contiguous genetic markers in case subjects compared with those in control subjects. The second approach tests for the run of homozygosity in case-series studies. SNP marker data with and without linkage disequilibrium were simulated from chromosome 2q (80cM--180cM) of the HapMap. Analyses for simulation studies will be presented.